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- PDB-4pld: Human Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its ... -

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Basic information

Entry
Database: PDB / ID: 4pld
TitleHuman Nuclear Receptor Liver Receptor Homologue-1, LRH-1, in its apo State Bound to a Fragment of Human TIF-2
Components
  • Nuclear receptor coactivator 2
  • Nuclear receptor subfamily 5 group A member 2
KeywordsTRANSCRIPTION / Nuclear Receptor / apo
Function / homology
Function and homology information


positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation ...positive regulation of glucocorticoid biosynthetic process / zygotic genome activation / positive regulation of tendon cell differentiation / morula formation / Regulation of gene expression in early pancreatic precursor cells / primary ovarian follicle growth / pancreas morphogenesis / inner cell mass cell differentiation / tissue development / acinar cell differentiation / Sertoli cell development / positive regulation of stem cell differentiation / positive regulation of T cell anergy / embryonic cleavage / bile acid metabolic process / embryo development ending in birth or egg hatching / exocrine pancreas development / cartilage development / negative regulation of chondrocyte differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / homeostatic process / locomotor rhythm / calcineurin-mediated signaling / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / somatic stem cell population maintenance / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of viral genome replication / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / hormone-mediated signaling pathway / : / positive regulation of adipose tissue development / neurogenesis / Regulation of lipid metabolism by PPARalpha / positive regulation of T cell proliferation / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cholesterol homeostasis / cellular response to leukemia inhibitory factor / nuclear receptor binding / transcription coregulator binding / negative regulation of smoothened signaling pathway / SUMOylation of intracellular receptors / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / positive regulation of T cell activation / phospholipid binding / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 ...Nuclear hormone receptor family 5 / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nuclear receptor subfamily 5 group A member 2 / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsMusille, P.M. / Ortlund, E.A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity.
Authors: Musille, P.M. / Kossmann, B.R. / Kohn, J.A. / Ivanov, I. / Ortlund, E.A.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 5 group A member 2
B: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5953
Polymers29,9812
Non-polymers6151
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-7 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.813, 65.681, 83.482
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor subfamily 5 group A member 2 / Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor ...Alpha-1-fetoprotein transcription factor / B1-binding factor / hB1F / CYP7A promoter-binding factor / Hepatocytic transcription factor / Liver receptor homolog 1 / LRH-1


Mass: 28271.668 Da / Num. of mol.: 1 / Fragment: UNP residues 301-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR5A2, B1F, CPF, FTF / Production host: Escherichia coli (E. coli) / References: UniProt: O00482
#2: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1708.931 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 740-753 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.7-1 M di-Sodium Malonate, 0.1 M HEPES pH 7.4, 0.5% Jeffamine ED-2001
PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 25933 / % possible obs: 99.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.4 Å2 / Net I/σ(I): 18.99
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.8 / % possible all: 96.22

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yok

1yok


Resolution: 1.75→26.691 Å / FOM work R set: 0.8468 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 2000 7.71 %Random selection
Rwork0.1871 23928 --
obs0.19 25928 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.27 Å2 / Biso mean: 24.32 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.75→26.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 100 137 2263
Biso mean--32.08 29.35 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082107
X-RAY DIFFRACTIONf_angle_d1.4122856
X-RAY DIFFRACTIONf_chiral_restr0.284328
X-RAY DIFFRACTIONf_plane_restr0.005358
X-RAY DIFFRACTIONf_dihedral_angle_d16.921790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7504-1.79420.27611330.23071591X-RAY DIFFRACTION95
1.7942-1.84270.28711410.2071688X-RAY DIFFRACTION99
1.8427-1.89690.25711400.21631679X-RAY DIFFRACTION100
1.8969-1.95810.23551420.19791689X-RAY DIFFRACTION100
1.9581-2.02810.23671410.18561687X-RAY DIFFRACTION100
2.0281-2.10930.23791430.17731707X-RAY DIFFRACTION100
2.1093-2.20520.27011400.18361690X-RAY DIFFRACTION100
2.2052-2.32140.19561430.16311704X-RAY DIFFRACTION100
2.3214-2.46680.21931420.17181710X-RAY DIFFRACTION100
2.4668-2.65710.22521440.17611717X-RAY DIFFRACTION100
2.6571-2.92410.24441440.19351718X-RAY DIFFRACTION100
2.9241-3.34660.24141460.19811751X-RAY DIFFRACTION100
3.3466-4.21370.18191470.17051759X-RAY DIFFRACTION100
4.2137-100.22281540.19991838X-RAY DIFFRACTION99

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